Bio::SeqFeature::Computation extends the Generic seqfeature object witha set of computation related fields and a more flexible set of storingmore types of score and subseqfeatures. It is compatible with the GenericSeqFeature object.The new way of storing score values is similar to the tag structure in the Generic object. For storing sets of subseqfeatures the array containg thesubseqfeatures is now a hash which contains arrays of seqfeaturesBoth the score and subSeqfeature methods can be called in exactly the sameway, the value's will be stored as a 'default' score or subseqfeature.

Title : has_score Usage : $value = $self->has_score('some_score') Function: Tests wether a feature contains a score Returns : TRUE if the SeqFeature has the score, and FALSE otherwise. Args : The name of a score

Title : each_score_value Usage : @values = $gsf->each_score_value('note'); Function: Returns a list of all the values stored under a particular score. Returns : A list of scalars Args : The name of the score

Title : computation_id Usage : $computation_id = $feat->computation_id() $feat->computation_id($computation_id) Function: get/set on program name information Returns : string Args : none if get, the new value if set

Title : program_name Usage : $program_name = $feat->program_name() $feat->program_name($program_name) Function: get/set on program name information Returns : string Args : none if get, the new value if set

Title : database_name Usage : $database_name = $feat->database_name() $feat->database_name($database_name) Function: get/set on program name information Returns : string Args : none if get, the new value if set

Title : get_SeqFeature_type Usage : $SeqFeature_type = $feat->get_SeqFeature_type() $feat->get_SeqFeature_type($SeqFeature_type) Function: Get SeqFeature type which is automatically set when adding a computation (SeqFeature) to a computation object Returns : SeqFeature_type (string) Args : none if get, the new value if set

Title : add_SeqFeature Usage : $feat->add_SeqFeature($subfeat); $feat->add_SeqFeature($subfeat,'seqfeature_type') $feat->add_SeqFeature($subfeat,'EXPAND') $feat->add_SeqFeature($subfeat,'EXPAND','seqfeature_type') Function: adds a SeqFeature into a specific subSeqFeature array. with no 'EXPAND' qualifer, subfeat will be tested as to whether it lies inside the parent, and throw an exception if not. If EXPAND is used, the parents start/end/strand will be adjusted so that it grows to accommodate the new subFeature, optionally a seqfeature type can be defined. Returns : nothing Args : An object which has the SeqFeatureI interface (optional) 'EXPAND' (optional) 'SeqFeature_type'

Title : remove_SeqFeatures Usage : $sf->remove_SeqFeatures $sf->remove_SeqFeatures('SeqFeature_type'); Function: Removes all sub SeqFeature or all sub SeqFeatures of a specified type (if you want to remove a more specific subset, take an array of them all, flush them, and add back only the guys you want) Example : Returns : none Args : none

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